chr12-48905046-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_033124.5(CCDC65):c.233A>T(p.His78Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000322 in 1,614,112 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_033124.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC65 | NM_033124.5 | c.233A>T | p.His78Leu | missense_variant | 2/8 | ENST00000320516.5 | |
CCDC65 | NM_001286957.2 | c.-197A>T | 5_prime_UTR_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC65 | ENST00000320516.5 | c.233A>T | p.His78Leu | missense_variant | 2/8 | 1 | NM_033124.5 | P2 | |
CCDC65 | ENST00000266984.9 | c.233A>T | p.His78Leu | missense_variant | 2/9 | 5 | A2 | ||
CCDC65 | ENST00000552942.5 | c.233A>T | p.His78Leu | missense_variant | 2/6 | 5 | |||
CCDC65 | ENST00000547861.5 | c.*64A>T | 3_prime_UTR_variant, NMD_transcript_variant | 2/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00168 AC: 256AN: 152196Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000410 AC: 103AN: 251396Hom.: 1 AF XY: 0.000368 AC XY: 50AN XY: 135874
GnomAD4 exome AF: 0.000179 AC: 262AN: 1461798Hom.: 2 Cov.: 31 AF XY: 0.000160 AC XY: 116AN XY: 727196
GnomAD4 genome AF: 0.00169 AC: 257AN: 152314Hom.: 2 Cov.: 32 AF XY: 0.00167 AC XY: 124AN XY: 74470
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 27 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at